BLASTP 2.2.18 [Mar-02-2008] Reference: Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schaffer, Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), "Gapped BLAST and PSI-BLAST: a new generation of protein database search programs", Nucleic Acids Res. 25:3389-3402. Reference for compositional score matrix adjustment: Altschul, Stephen F., John C. Wootton, E. Michael Gertz, Richa Agarwala, Aleksandr Morgulis, Alejandro A. Schaffer, and Yi-Kuo Yu (2005) "Protein database searches using compositionally adjusted substitution matrices", FEBS J. 272:5101-5109. Query= 0256.0059.p (445 letters) Database: pfamseq 9,421,015 sequences; 3,060,696,203 total letters Searching..................................................done Score E Sequences producing significant alignments: (bits) Value B3KL88.1 B3KL88_9BACI RNA binding S1 domain protein 556 e-156 B1DJ71.1 B1DJ71_9BACL RNA binding S1 domain protein 484 e-135 C0ZCB1.1 C0ZCB1_BREBN 30S ribosomal protein S1 homolog 370 e-100 Q9KCD6.1 Q9KCD6_BACHD 30S ribosomal protein S1 363 2e-98 C3BI75.1 C3BI75_9BACI 30S ribosomal protein S1 352 4e-95 >B3KL88.1 B3KL88_9BACI RNA binding S1 domain protein Length = 405 Score = 556 bits (1433), Expect = e-156, Method: Compositional matrix adjust. Identities = 284/402 (70%), Positives = 319/402 (79%), Gaps = 5/402 (1%) Query: 43 NEEEVTSQEGL-EIISLKKGDTVKGTIVKIEDNQAYVSIGYKYDGVIPIRELSSVQLDNX 101 N+E +QE L +I+SLKKGDTVKGTIVK+EDNQAYVSIGYKYDGVIP+RELSSVQLDN Sbjct: 7 NQEAAENQEQLDQIVSLKKGDTVKGTIVKLEDNQAYVSIGYKYDGVIPVRELSSVQLDNA 66 Query: 102 XXXXXXXXXXXCKVVSINDNKESLVLSKRAVDSEKSWEDLEKYFASQEAFEVTVADVVKG 161 CKVVSIND+KESLVLSKRA+D+E SW++LEK+FA Q+ FEVTVADVVKG Sbjct: 67 SDAVQVGQEVECKVVSINDDKESLVLSKRAIDTENSWDELEKHFADQDVFEVTVADVVKG 126 Query: 162 GLVADVGARGFIPASMVERHFVEDFSDYKGRTLRVKVKELDRENSKVILSAKEVLEEEFE 221 GLVADVGARGFIPASMVERHFVEDFSDYKGRTLRVKVKELDREN+KVILS K+VLEEEFE Sbjct: 127 GLVADVGARGFIPASMVERHFVEDFSDYKGRTLRVKVKELDRENNKVILSQKDVLEEEFE 186 Query: 222 ANKQKIMSELSEGQIIEGTVQRLTQFGAFXXXXXXXXLVHVSEIAWNHVEKPSDXXXXXX 281 ANKQK+MSEL +GQ++EGTVQRLTQFGAF LVHVSEIAW+HV+KPSD Sbjct: 187 ANKQKVMSELQDGQVLEGTVQRLTQFGAFVDVGGVDGLVHVSEIAWSHVDKPSDVLSEGD 246 Query: 282 XXXXXXXXXXXXXGKISLSIKAAAPGPWDSAAGKINIGDVVTGEVKRLVNFGAFVELLPG 341 GKISLSIKAAAPGPW++A + N GD+VTG VKRLV FGAFVEL PG Sbjct: 247 QVRVKVLKVDPEKGKISLSIKAAAPGPWETAGEQFNTGDIVTGVVKRLVTFGAFVELAPG 306 Query: 342 VEGLVHISQISHKHIGTPHEVLKEGQEVQVKVLDFNPSEKRVSLSIKXXXXXXXXXXXXX 401 VEGLVHISQISHKHIGTP EVLKEGQEVQVKVLD N SE+R+SLSIK Sbjct: 307 VEGLVHISQISHKHIGTPQEVLKEGQEVQVKVLDINTSEQRISLSIKETEEAPAQAPRAE 366 Query: 402 XSNNRDRAPK-EVLNNPNVSLSNEGLSFTLAERFGDKLDKFK 442 + + PK ++ +NPNVSL+N+G+S TL ERFGDKL KFK Sbjct: 367 KPS---KGPKIDLKDNPNVSLNNQGMSVTLGERFGDKLSKFK 405 >B1DJ71.1 B1DJ71_9BACL RNA binding S1 domain protein Length = 411 Score = 484 bits (1246), Expect = e-135, Method: Compositional matrix adjust. Identities = 251/396 (63%), Positives = 291/396 (73%), Gaps = 8/396 (2%) Query: 55 IISLKKGDTVKGTIVKIEDNQAYVSIGYKYDGVIPIRELSSVQLDNXXXXXXXXXXXXCK 114 +SLKKGDTVKGTI+KI+DNQAYVS+GYKYDGVIP+RELS+VQLDN K Sbjct: 16 FVSLKKGDTVKGTIIKIDDNQAYVSLGYKYDGVIPVRELSAVQLDNANDAVQVGQEVELK 75 Query: 115 VVSINDNKESLVLSKRAVDSEKSWEDLEKYFASQEAFEVTVADVVKGGLVADVGARGFIP 174 VVSI+D KE LVLSKR +D E++W+ L+ F S E FEV VADVVKGGLVADVG RGFIP Sbjct: 76 VVSIDDEKEKLVLSKRLIDGERAWDGLQSRFESGEVFEVAVADVVKGGLVADVGVRGFIP 135 Query: 175 ASMVERHFVEDFSDYKGRTLRVKVKELDRENSKVILSAKEVLEEEFEANKQKIMSELSEG 234 ASMVERHFVEDFSDYKGRTLRVKVKE+DREN+KVILSAK+VL+ EFE NKQ +++ L G Sbjct: 136 ASMVERHFVEDFSDYKGRTLRVKVKEIDRENNKVILSAKDVLDAEFEQNKQHVIAGLQVG 195 Query: 235 QIIEGTVQRLTQFGAFXXXXXXXXLVHVSEIAWNHVEKPSDXXXXXXXXXXXXXXXXXXX 294 +EGTVQRLT FGAF LVHVSE++W HV P D Sbjct: 196 AQLEGTVQRLTPFGAFVDIGGIDGLVHVSELSWQHVAHPKDVVSEGQQVTVKVLKVDPAA 255 Query: 295 GKISLSIKAAAPGPWDSAAGKINIGDVVTGEVKRLVNFGAFVELLPGVEGLVHISQISHK 354 GKISLSIKAA PGPW+SAAG+ N+GD+VTG V+RLV FGAFVE+ PGVEGLVHISQI+H+ Sbjct: 256 GKISLSIKAAQPGPWESAAGQFNVGDIVTGTVRRLVTFGAFVEIAPGVEGLVHISQIAHR 315 Query: 355 HIGTPHEVLKEGQEVQVKVLDFNPSEKRVSLSIKXXXXXXXXXXXXXXSN----NRDRAP 410 HI TP EVLKEGQEVQ KVLDFNP+EKRVSLSIK R+R P Sbjct: 316 HIATPFEVLKEGQEVQAKVLDFNPAEKRVSLSIKETEEAPEQPAAEQAPKAGRPQRERTP 375 Query: 411 K----EVLNNPNVSLSNEGLSFTLAERFGDKLDKFK 442 + ++ NNPNVSL++ +S++LAERFGDKL K K Sbjct: 376 QVKPEDLGNNPNVSLNSSSMSYSLAERFGDKLSKLK 411 >C0ZCB1.1 C0ZCB1_BREBN 30S ribosomal protein S1 homolog Length = 389 Score = 370 bits (949), Expect = e-100, Method: Compositional matrix adjust. Identities = 193/382 (50%), Positives = 240/382 (62%), Gaps = 9/382 (2%) Query: 61 GDTVKGTIVKIEDNQAYVSIGYKYDGVIPIRELSSVQLDNXXXXXXXXXXXXCKVVSIND 120 GD VK T+ K+ED QA V +GYKYDG+IPI ELS + ++ KV+ +ND Sbjct: 17 GDVVKATVTKVEDKQALVDLGYKYDGLIPISELSPLHVEKVSDVVAVGDTFEVKVIKLND 76 Query: 121 NKESLVLSKRAVDSEKSWEDLEKYFASQEAFEVTVADVVKGGLVADVGARGFIPASMVER 180 KE LV+SK+AV E SW DLE+ + E E V +VVKGGLV DVG RGFIPASMVER Sbjct: 77 EKEELVVSKKAVAMESSWSDLEQKMQAGEIIEAAVKEVVKGGLVVDVGVRGFIPASMVER 136 Query: 181 HFVEDFSDYKGRTLRVKVKELDRENSKVILSAKEVLEEEFEANKQKIMSELSEGQIIEGT 240 HFVEDFSDYKG+TL +KV E+D+E +KVILS K VLE+E + KQ IM ++ GQ++EGT Sbjct: 137 HFVEDFSDYKGKTLALKVVEMDKEKNKVILSHKAVLEDEVKVQKQSIMDKIQVGQVLEGT 196 Query: 241 VQRLTQFGAFXXXXXXXXLVHVSEIAWNHVEKPSDXXXXXXXXXXXXXXXXXXXGKISLS 300 VQR+T FG F LVHVSE+AWN V+KPSD +I LS Sbjct: 197 VQRMTDFGVFVDIGGVDGLVHVSELAWNRVDKPSDVVKEGDKVKVKVLKIDRENERIGLS 256 Query: 301 IKAAAPGPWDSAAGKINIGDVVTGEVKRLVNFGAFVELLPGVEGLVHISQISHKHIGTPH 360 IK GPW S A G ++ G VKRLV+FGAF+EL PG+EGLVHISQI+++ + TP Sbjct: 257 IKETQAGPWASVAEDFKAGSILNGTVKRLVSFGAFIELAPGIEGLVHISQIANRRVNTPS 316 Query: 361 EVLKEGQEVQVKVLDFNPSEKRVSLSIKXXXXXXXXXXXXXXSNNRDRAPKEVLNNPNVS 420 EVLKEGQEVQVKVLD P E+R+SLSI+ + + +E Sbjct: 317 EVLKEGQEVQVKVLDVVPQEQRISLSIRAVEEDRVEQAERASKREQQQFTQE-------- 368 Query: 421 LSNEGLSFTLAERFGDKLDKFK 442 +N+ + TL E FGD DKFK Sbjct: 369 -NNQPMGVTLGELFGDLKDKFK 389 >Q9KCD6.1 Q9KCD6_BACHD 30S ribosomal protein S1 Length = 383 Score = 363 bits (931), Expect = 2e-98, Method: Compositional matrix adjust. Identities = 194/389 (49%), Positives = 251/389 (64%), Gaps = 16/389 (4%) Query: 54 EIISLKKGDTVKGTIVKIEDNQAYVSIGYKYDGVIPIRELSSVQLDNXXXXXXXXXXXXC 113 E+ S GD V G + K+ED QA+V +G+K DG+IPI ELSS+ ++ Sbjct: 11 EMKSFSVGDVVSGKVTKVEDKQAFVDVGFKVDGIIPISELSSLHVEKVSDVLSEGDELEL 70 Query: 114 KVVSINDNKESLVLSKRAVDSEKSWEDLEKYFASQEAFEVTVADVVKGGLVADVGARGFI 173 KV+ + D++ L+LSKRAV +EK+WE L+ S E E VADVVKGGLV D+G RGFI Sbjct: 71 KVLKVEDDE--LILSKRAVQAEKAWETLQAALDSGEVIEAEVADVVKGGLVVDLGVRGFI 128 Query: 174 PASMVERHFVEDFSDYKGRTLRVKVKELDRENSKVILSAKEVLEEEFEANKQKIMSELSE 233 PAS+VERH+VEDFSDYKGRTLR+KV ELD+E +K+ILS + VL+EE EA K+++++ L Sbjct: 129 PASLVERHYVEDFSDYKGRTLRLKVVELDKEANKLILSQRAVLDEEVEAKKKEVLASLQP 188 Query: 234 GQIIEGTVQRLTQFGAFXXXXXXXXLVHVSEIAWNHVEKPSDXXXXXXXXXXXXXXXXXX 293 G ++EGTVQRLT FGAF LVH+S++A + VE P++ Sbjct: 189 GDVVEGTVQRLTDFGAFVDVGGVDGLVHISQLAHHRVETPAEVVKEGDAVKVKVLSVDPD 248 Query: 294 XGKISLSIKAAAPGPWDSAAGKINIGDVVTGEVKRLVNFGAFVELLPGVEGLVHISQISH 353 ++SLSIK PGPW+ G I GDV+ G VKRLV+FGAFVE+ PGVEGLVHISQI++ Sbjct: 249 SERVSLSIKETLPGPWEQVEGTIQPGDVIEGTVKRLVSFGAFVEVAPGVEGLVHISQIAN 308 Query: 354 KHIGTPHEVLKEGQEVQVKVLDFNPSEKRVSLSIKXXXXXXXXXXXXXXSNNRDRAPKEV 413 +HIGTP EVL EG+ VQ KVLD N SEKR+SLSI+ SN DR EV Sbjct: 309 RHIGTPGEVLSEGERVQAKVLDVNISEKRISLSIR-------ELLDDAGSNQSDR---EV 358 Query: 414 LNNPNVSLSNEGLSFTLAERFGDKLDKFK 442 + N E F+L + GD+L K+K Sbjct: 359 YESTN----EESSGFSLGDMIGDELKKYK 383 >C3BI75.1 C3BI75_9BACI 30S ribosomal protein S1 Length = 382 Score = 352 bits (904), Expect = 4e-95, Method: Compositional matrix adjust. Identities = 178/346 (51%), Positives = 243/346 (70%), Gaps = 8/346 (2%) Query: 43 NEEEVTSQEGLEIISLKKGDTVKGTIVKIEDNQAYVSIGYKYDGVIPIRELSSVQLDNXX 102 NEE V S+ +L+ GD V G++ K+E+ Q V++GYK DGVIPI EL++V ++ Sbjct: 6 NEEVVDSK------ALQVGDVVTGSVTKVEEKQVLVNVGYKTDGVIPISELANVHIEKAS 59 Query: 103 XXXXXXXXXXCKVVSINDNKESLVLSKRAVDSEKSWEDLEKYFASQEAFEVTVADVVKGG 162 KV+ + D+ LVLSKRAVD+EK+W +L++ F S E F+VTV D+V GG Sbjct: 60 DVVKLDQNLELKVIKLEDD--DLVLSKRAVDAEKAWVELQEKFTSGEVFDVTVKDIVNGG 117 Query: 163 LVADVGARGFIPASMVERHFVEDFSDYKGRTLRVKVKELDRENSKVILSAKEVLEEEFEA 222 LV D+G RGFIPAS+VE H+VEDF+DYKG+TL VK+ ELDRE ++VILS K V+E+E E+ Sbjct: 118 LVVDLGVRGFIPASLVEMHYVEDFTDYKGKTLAVKIVELDREKNRVILSHKAVVEQELES 177 Query: 223 NKQKIMSELSEGQIIEGTVQRLTQFGAFXXXXXXXXLVHVSEIAWNHVEKPSDXXXXXXX 282 K++ +S L EG ++EGTVQRLT FGAF LVH+S+I+ + VE+PSD Sbjct: 178 KKKEAISSLKEGDVVEGTVQRLTDFGAFVNVGNVDGLVHISQISHDRVEQPSDVLTQGQS 237 Query: 283 XXXXXXXXXXXXGKISLSIKAAAPGPWDSAAGKINIGDVVTGEVKRLVNFGAFVELLPGV 342 +ISLSIKAA PGPW++ + ++ GD+ G VKR+V FGAFVE+LPGV Sbjct: 238 VKVKVLSVDADTQRISLSIKAAQPGPWENVSAEVKAGDIREGIVKRIVTFGAFVEILPGV 297 Query: 343 EGLVHISQISHKHIGTPHEVLKEGQEVQVKVLDFNPSEKRVSLSIK 388 EGLVH+SQI+++H+ P+EVL+ GQEV+VKVL+ + +EKR+SLSIK Sbjct: 298 EGLVHVSQIANRHVKNPNEVLEMGQEVKVKVLEVHAAEKRISLSIK 343 Score = 56.2 bits (134), Expect = 6e-06, Method: Compositional matrix adjust. Identities = 48/183 (26%), Positives = 94/183 (51%), Gaps = 6/183 (3%) Query: 44 EEEVTSQEGLEIISLKKGDTVKGTIVKIEDNQAYVSIGYKYDGVIPIRELSSVQLDNXXX 103 E+E+ S++ I SLK+GD V+GT+ ++ D A+V++G DG++ I ++S +++ Sbjct: 172 EQELESKKKEAISSLKEGDVVEGTVQRLTDFGAFVNVG-NVDGLVHISQISHDRVEQPSD 230 Query: 104 XXXXXXXXXCKVVSINDNKESLVLSKRAVDSEKSWEDLEKYFASQEAFEVTVADVVKGGL 163 KV+S++ + + + LS +A WE++ + + E V +V G Sbjct: 231 VLTQGQSVKVKVLSVDADTQRISLSIKAAQP-GPWENVSAEVKAGDIREGIVKRIVTFGA 289 Query: 164 VADV--GARGFIPASMVERHFVEDFSDY--KGRTLRVKVKELDRENSKVILSAKEVLEEE 219 ++ G G + S + V++ ++ G+ ++VKV E+ ++ LS KE +EE Sbjct: 290 FVEILPGVEGLVHVSQIANRHVKNPNEVLEMGQEVKVKVLEVHAAEKRISLSIKEAVEEN 349 Query: 220 FEA 222 E Sbjct: 350 NET 352 Database: pfamseq Posted date: Aug 5, 2010 3:22 PM Number of letters in database: 3,060,696,203 Number of sequences in database: 9,421,015 Lambda K H 0.312 0.131 0.358 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 9421015 Number of Hits to DB: 1,960,637,222 Number of extensions: 68553096 Number of successful extensions: 181725 Number of sequences better than 1.0e-05: 3792 Number of HSP's gapped: 166031 Number of HSP's successfully gapped: 5665 Length of query: 445 Length of database: 3,060,696,203 Length adjustment: 139 Effective length of query: 306 Effective length of database: 1,751,175,118 Effective search space: 535859586108 Effective search space used: 535859586108 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.2 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 42 (21.8 bits) S2: 133 (55.8 bits)